Table 2.

Divergence and polymorphism in reference genes assessed by McDonald-Kreitman test, stratified by level of cross-genus conservation

Conservation level	dN/dS	Adjusted dN/dS		Synonymous	Non-synonymous	Chi-squared	Neutrality Index
Identical	0.030	0.034	D	839	101	8.3 × 10-15	5.6
			P	52	35
Semi-conserved	0.21	0.24	D	186	174	0.22	1.6
			P	12	18
Non-conserved	0.35	0.39	D	90	118	0.38	1.5
			P	7	14
Non-aligned	0.55	0.64	D	155	402	0.74	1.1
			P	12	35
Total	0.15	0.17	D	1270	795	9.5 × 10-6	2.0
			P	83	102

dN/dS ratios refer to P. falciparum /P. reichenowi divergence. Conservation levels were based on BLOSUM62 score in P. falciparum - P. chabaudi alignments; identical (+4 and above), semi-conserved (0 to +3), non-conserved (-4 to -1) and non-aligned. Adjusted dN/dS ratios were derived based on the transition: transversion ratio measured at 4-fold degenerate sites (see Table 4). D = divergent mutations, P = polymorphisms. Chi-squared and Neutrality Index are the outputs of the McDonald-Kreitman test; neutrality index indicates the extent to which the levels of variation depart from the expected in the neutral model with values greater than 1 indicating an excess of polymorphism and hence negative selection.